Reproducible Analyses

 

CrustyBase v.2.0: new features and enhanced utilities to support open science

Background Transcriptomes present a rich, multi-dimensional subset of genomics data. They provide broad insights into genetic sequence, and more significantly gene expression, across biological samples. This technology is frequently employed for …

Do organisms need an impact factor? Citations of key biological resources including model organisms reveal usage patterns and impact

Research resources like transgenic animals and antibodies are the workhorses of biomedicine, enabling investigators to relatively easily study specific disease conditions. As key biological resources, transgenic animals and antibodies are often …

Endorsement of open science practices by dental journals: A meta-research study

Objectives This study evaluates the endorsement of open science practices by dental journals. Materials and methods This was a meta-research study that included journals listed in the 2021 Journal Citation Reports under Dentistry. A comprehensive …

Maximizing Data Transparency with Rigor Icons

Scientific meetings are an important venue for disseminating findings, but space and time for experimental design details is often limited. Thus, to facilitate increased transparency in scientific presentations, rigor icons can quickly and easily …

Open science and the climate crisis

In 2009, the climate research community was rocked by the Climategate controversy, an email leak that allegedly provided evidence of data manipulation [1]. While that allegation was shown to be unsubstantiated [2], it focused the community’s …

Open Science Practices in Psychiatric Genetics: A Primer

Open science ensures that research is transparently reported and freely accessible for all to assess and collaboratively build on. Psychiatric genetics has led among the health sciences in implementing some open science practices in common study …

The reporting completeness and transparency of systematic reviews of prognostic prediction models for COVID-19 was poor: a methodological overview of systematic reviews

Objectives To conduct a methodological overview of reviews to evaluate the reporting completeness and transparency of systematic reviews (SRs) of prognostic prediction models (PPMs) for COVID-19. Study Design and Setting MEDLINE, Scopus, Cochrane …

Toward a 21st Century National Data Infrastructure: Managing Privacy and Confidentiality Risks with Blended Data

Protecting privacy and ensuring confidentiality in data is a critical component of modernizing our national data infrastructure. The use of blended data - combining previously collected data sources - presents new considerations for responsible data …

A Replication Crisis in Methodological Research?

Statisticians have been keen to critique statistical aspects of the “replication crisis” in other scientific disciplines. But new statistical tools are often published and promoted without any thought to replicability. This needs to change, argue …

Building reproducible bridges to cross the “valley of death”

Research is cumulative. New investigations build on, challenge, or qualify claims based on prior evidence. When we have limited evidence, it is normal that some explanations are wrong and need to be refined or reconsidered. This self-corrective …
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